AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_aful_reg_100.orf -o00340_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: AF0212 25 histidinol dehydrogenase (hisD) Input sequences: #1 AF0140 123 ubiquinone/menaquinone biosynthesis methyltransferase (ubiE) #2 AF0590 185 ATP phosphoribosyltransferase (hisG) #3 AF0727 97 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #4 AF0818 102 acylphosphatase (acyP) #5 AF0986 30 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA-2) #6 AF0987 109 conserved hypothetical protein #7 AF1642 50 histidyl-tRNA synthetase (hisS) #8 AF1778 105 stage V sporulation protein (spoVG) #9 AF1779 57 2-hydroxyacid dehydrogenase, putative #10 AF1948 152 A. fulgidus predicted coding region AF1948 #11 AF1950 54 phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphohydrolase (hisIE) #12 AF2265 48 imidazoleglycerol-phosphate synthase, subunit H (hisH) Motif number 1 TGAATCCTTAAGCCCTTTTCTTCT 1 110 1 AGCCCTTTTC 0.833118 -14 AAGTAGACCTTGACCTTTTCGTTCTGCATC 2 46 0 TGACCTTTTC 0.930857 -140 TGACTTTATTTAAATTTTTTGGATTTTCAG 3 44 1 TAAATTTTTT 0.602845 -54 TTTTTTAACCTTTTCTTCCCACTCC 5 6 1 TAACCTTTTC 0.97707 -25 ACTATTTTGAAAAACTTTTTATTGATAAAT 6 27 0 AAAACTTTTT 0.936287 -83 CTCAACTCTAAAACCTTTTAAACACCCTTG 7 18 1 AAACCTTTTA 0.922633 -33 TTTTGCTTCAAAACCTTTTTATCTTTTCTG 9 24 1 AAACCTTTTT 0.982716 -34 AAAAGCCCACAAAACTTTTCGAAACCTATT 10 109 1 AAAACTTTTC 0.963351 -44 AAACTTTTCGAAACCTATTTAAAGAAAAAG 10 120 1 AAACCTATTT 0.921532 -33 GAAAAATTTTTAACTTTTTCTTTAAATAGG 10 133 0 TAACTTTTTC 0.894555 -20 GAAAAAGTTAAAAATTTTTC 10 143 1 AAAATTTTTC 0.840249 -10 TACAACACAAAAACCTATTTTTACCACCCG 11 22 1 AAACCTATTT 0.921532 -33 AACCTTAATTAATCCTTTTTCTCAAGCCCT 12 25 1 AATCCTTTTT 0.869469 -24 ********** Masking position 6 Map Score: 17.8955 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 462 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 2 CGCTCCTTTGCTTAAATCGCCCATTGAATT 1 22 1 CTTAAATCGC 0.837316 -102 ATCCTGGCATCTTTTTACCCAAAAAACATG 1 61 0 CTTTTTACCC 0.570169 -63 CTTAAGGATTCATTTATACCTTTCGTTTAC 1 92 0 CATTTATACC 0.802875 -32 GCTTATAAAACCCACCGCTTT 2 2 1 CTTATAAAAC 0.639264 -184 TGACGGTCATCTTGAAAAGCCAATCTGGGA 2 78 1 CTTGAAAAGC 0.807559 -108 TCTGGGACGCCTTAATTACCGCTGGATACA 2 101 1 CTTAATTACC 0.888395 -85 CTGCTTAAAAACCAGCTTGGGGT 2 173 0 CTTAAAAACC 0.977618 -13 AGAATTCAAACTTATATACCGCAGGCAAAA 4 74 1 CTTATATACC 0.938447 -29 TTATTGAAACCATCAATCCCTACCTCCGGA 6 56 1 CATCAATCCC 0.734888 -54 ATTCGCTCAACTCTAAAACCTTTTAAACAC 7 13 1 CTCTAAAACC 0.858793 -38 ACCACGCTCTCATAATAAGCCC 8 3 0 CATAATAAGC 0.713245 -103 AATCAAAATTCTTATATACCACTTTGTTTG 8 55 1 CTTATATACC 0.938447 -51 TTGGCTTTTGCTTCAAAACCTTTTTATCTT 9 19 1 CTTCAAAACC 0.949448 -39 TCCAATTTTCCATTAAAAGCCCACAAAACT 10 95 1 CATTAAAAGC 0.827518 -58 TTTTTTACAACACAAAAACCTATTTTTACC 11 17 1 CACAAAAACC 0.857942 -38 ********** Masking position 1 Map Score: 13.8348 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 589 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 3 AAAGATGCCAGGATGGTAAACGAAAGGTAT 1 77 1 GGATGGTAAA 0.918282 -47 TTAAAGCGGTGGGTTTTATAAGC 2 4 0 GGGTTTTATA 0.653574 -182 GTCCCAGATTGGCTTTTCAAGATGACCGTC 2 79 0 GGCTTTTCAA 0.804525 -107 AACCAGCTTGGGGTGGTCAACGTCAATGAG 2 157 0 GGGTGGTCAA 0.955985 -29 CACCCCAAGCTGGTTTTTAAGCAG 2 172 1 TGGTTTTTAA 0.766571 -14 TAAATTTTTTGGATTTTCAGTAAGATTTAT 3 54 1 GGATTTTCAG 0.871009 -44 GCTTCGGCAAGGGTGTTTAAAAGGTTTTAG 7 25 0 GGGTGTTTAA 0.97287 -26 AAATTTGAAAGGAGGGTTAGAA 8 94 1 GGAGGGTTAG 0.761194 -12 AAAAGTCCACTGATTTTAAAAAATGAAAAG 10 11 0 TGATTTTAAA 0.583584 -142 TAAAATCAGTGGACTTTTAACAAGTTCACA 10 23 1 GGACTTTTAA 0.861569 -130 ATGGAAAATTGGAGGTTTAGGGAAGTCTAA 10 78 0 GGAGGTTTAG 0.812765 -75 AAAGTTTTGTGGGCTTTTAATGGAAAATTG 10 97 0 GGGCTTTTAA 0.908772 -56 TAAATTGGCCGGGTGGTAAAAATAGGTTTT 11 31 0 GGGTGGTAAA 0.947329 -24 ********** Masking position 7 Map Score: 8.60712 Number of sites scoring better than the average of aligned sites = 615 Number in coding regions = 529 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 4 TCATCTTGAAAAGCCAATCTGGGACGCCTT 2 84 1 AAGCCAATCT 0.956231 -102 GACACAAGCTCAAGAAATCTGGAGGTGTT 3 10 0 CAAGAAATCT 0.676238 -88 AATTTAAATAAAGTCAATCTGACACAAGCT 3 30 0 AAGTCAATCT 0.974735 -68 AAACTCAGTTAAATAAATCTTACTGAAAAT 3 66 0 AAATAAATCT 0.838189 -32 AATTGCTATGCAGGCAAACTATTTATATGA 4 14 1 CAGGCAAACT 0.939597 -89 CATACAAAAGAATTCAAACTTATATACCGC 4 66 1 AATTCAAACT 0.880852 -37 TTTTATTGATAAATCAATCTTCATTAATCT 6 11 0 AAATCAATCT 0.967695 -99 ACGTTTCCTGCAATCAAAATTCTTATATAC 8 44 1 CAATCAAAAT 0.650855 -62 TTTGAAGCAAAAGCCAAACTCTTAA 9 6 0 AAGCCAAACT 0.956231 -52 CGAAGTTCGAAAATCATACTTTAGACTTCC 10 58 1 AAATCATACT 0.808307 -95 ********** Masking position 6 Map Score: 7.42215 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 199 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 CCTGTATCCAGCGGTAATTAAGGCGTCCCAG 2 102 0 GCGGTAATAA 0.981384 -84 CCTTTTGCCTGCGGTATATAAGTTTGAATTC 4 75 0 GCGGTATTAA 0.958218 -28 CTTAAGGAGTGGGAAGAAAAGGTTAAAAA 5 12 0 GTGGGAAAAA 0.948752 -19 TTATGAGAGCGTGGTAATTTAATCTAACGTT 8 18 1 GTGGTAATTA 0.942078 -88 CTCAAACAAAGTGGTATATAAGAATTTTGAT 8 56 0 GTGGTATTAA 0.971495 -50 AGGTTTTTGTGTTGTAAAAAATAGAAT 11 7 0 GTTGTAAAAA 0.886407 -48 AATTGGCCGGGTGGTAAAAATAGGTTTTTGT 11 28 0 GTGGTAAAAT 0.925875 -27 ******* *** Masking position 6 Map Score: 4.45954 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 34 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 TTTTAAATTTTCGCTCCTTTGCTTAA 1 7 1 ATTTTCGCTC 0.978141 -117 AGACCTTGACCTTTTCGTTCTGCATCATGG 2 42 0 CTTTTCGTTC 0.931511 -144 TTGTATGAATATTTTCGAACGAATTGAAAT 4 43 0 ATTTTCGAAC 0.976444 -60 AAATTCGCTCAACTCTAAAA 7 1 1 AAATTCGCTC 0.731436 -50 CTAAAGTATGATTTTCGAACTTCGGAACGT 10 52 0 ATTTTCGAAC 0.976444 -101 GCCCACAAAACTTTTCGAAACCTATTTAAA 10 113 1 CTTTTCGAAA 0.841683 -40 ********** Masking position 5 Map Score: 2.13739 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 90 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 AAGATGACCGTCAGGAAGTAGACCTTGACCT 2 60 0 TCGGAAGTAG 0.819519 -126 TTAAAAACCAGCTTGGGGTGGTCAACGTCAA 2 161 0 GCTGGGGTGG 0.965285 -25 GCTCAAGAAATCTGGAGGTGTT 3 2 0 TCGGAGGTGT 0.91096 -96 CCTCCAGATTTCTTGAGCTTGTGTCAGATTG 3 15 1 TCTGAGCTTG 0.92367 -83 TATACCGCAGGCAAAAGGTGGGGTT 4 88 1 GCAAAGGTGG 0.918242 -15 AATAGCTTTGTCCGGAGGTAGGGATTGATGG 6 65 0 TCGGAGGTAG 0.975998 -45 AAACACCCTTGCCGAAGCTTGAGC 7 37 1 GCGAAGCTTG 0.928533 -14 CGCAAGGGCTTGAGAAAAAGGA 12 37 0 GCAGGGCTTG 0.915747 -12 ** ******** Masking position 9 Map Score: 0.589098 Number of sites scoring better than the average of aligned sites = 1128 Number in coding regions = 1055 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 8 ********** No masking Map Score: -4.02577e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 ********** No masking Map Score: -4.02577e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: -4.02577e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0